follow the example of LC's intrepid or the Vaskohl (sp?) Klingon ship in KM...
youll need several models and some scripting to link them together... exactly how this is accomplished, i dont know personally - but if you search around the forums, i am certain it has been discussed before...
of course what youre wondering would be more complex than the ships in KM, since those ships only move "parts" of the ship and dont include any subsystems like torpedoes to fire or anything...